tbuckley/cabot-search huggingface dataset:
Rapid spread of a novel NDM-producing clone of Klebsiella pneumoniae CC147, Northern Italy, February to August 2023
Authors: Irene Mileto, Greta Petazzoni, Marta Corbella, Stefano Gaiarsa, Cristina Merla, Angela Kuka, Marina Ramus, Cristina Terulla, Micaela Brandolini, Antonio Piralla, Patrizia Cambieri, Fausto Baldanti
Journal: Eurosurveillance (2023)

New Delhi metallo-beta-lactamase (NDM)-producing Klebsiella pneumoniae ( Kp ) ST147 caused a large multi-hospital outbreak in Italy from 2018 to 2021. We describe a new ST6668 NDM-producing Kp clone, belonging to CC147, which rapidly spread across hospitals in the Pavia province (Northern Italy) from February to August 2023. Genomic analyses revealed that ST6668 is different from ST147 and fast evolving. As shown here, genomic surveillance programmes are useful for tracking the spread of new clones with reduced susceptibility to most antibiotics.
Visual Impairment Risk After Alcohol Abstinence in Patients With Newly Diagnosed Open-Angle Glaucoma
Authors: Yoon Jeong, Su Hwan Kim, Goneui Kang, Hyung-Jin Yoon, Young Kook Kim, Ahnul Ha
Journal: JAMA Network Open (2023)

Importance Recent studies indicate that alcohol consumption is linked to increased intraocular pressure and higher prevalence of open-angle glaucoma (OAG). However, there is insufficient evidence to establish any correlation between alcohol abstinence and improved outcomes in patients with OAG. Objective To evaluate the association between alcohol consumption status (and its changes) and risk of incident severe visual impairment (VI) or blindness in patients with newly diagnosed OAG. Design, Setting, and Participants This retrospective, nationwide, population-based cohort study used the Korean National Health Insurance Service’s claims and health examination database to enroll patients who were newly diagnosed with OAG between January 1, 2010, and December 31, 2011, and had been alcohol drinkers before their OAG diagnosis. The cohort was followed up until December 2020. The data were analyzed from February to December 2022. Exposures The patients were categorized into 2 groups based on their post–OAG diagnosis alcohol consumption status: sustainers and abstainers. The risks of severe VI or blindness were compared using weighted Cox proportional hazards regression models along with inverse probability of treatment weighting. Main Outcomes and Measures Incident severe VI or blindness. Results Among 13 643 patients with newly diagnosed OAG (mean [SD] age, 53.7 [11.9] years; 12 066 men [88.4%]) who were drinkers, 2866 (21.0%) quit drinking after the diagnosis. During 91 366 person-years of follow-up, patients abstaining from alcohol after their OAG diagnosis had a lower risk of severe VI or blindness than did those who had sustained drinking (adjusted hazard ratio [AHR] after inverse probability of treatment weighting, 0.63; 95% CI, 0.45-0.87). Among the sustained drinkers, both mild consumption (&amp;amp;lt;105 g/wk; AHR, 1.52; 95% CI, 1.01-2.28) and moderate to heavy consumption (≥105 g/wk; AHR, 1.78; 95% CI, 1.11-2.86) after OAG diagnosis were associated with higher risk of severe VI or blindness relative to abstainers. Frequent drinking (≥4 d/wk) also was associated with a higher risk of severe VI or blindness (AHR, 2.56; 95% CI, 1.52-4.33) compared with abstinence. Conclusions and Relevance In this cohort study of patients with OAG who were drinkers, abstaining from alcohol after an OAG diagnosis was associated with lower risk of severe VI or blindness. These findings suggest that lifestyle interventions, such as alcohol abstinence, could be essential for patients with newly diagnosed OAG.
Chemotherapy and Immune Checkpoint Blockade for Gastric and Gastroesophageal Junction Adenocarcinoma
Authors: Gulam A. Manji, Shing Lee, Armando Del Portillo, Michael May, Sarah Sta Ana, Emily Alouani, Naomi Sender, Tiffany Negri, Katarzyna Gautier, Liner Ge, Weijia Fan, Mengyu Xie, Amrita Sethi, Beth Schrope, Aik Choon Tan, Haeseong Park, Paul E. Oberstein, Manish A. Shah, Alexander G. Raufi
Journal: JAMA Oncology (2023)

Importance Combining immune checkpoint blockade (ICB) with chemotherapy improves outcomes in patients with metastatic gastric and gastroesophageal junction (G/GEJ) adenocarcinoma; however, whether this combination has activity in the perioperative setting remains unknown. Objective To evaluate the safety and preliminary activity of perioperative chemotherapy and ICB followed by maintenance ICB in resectable G/GEJ adenocarcinoma. Design, Setting, and Participants This investigator-initiated, multicenter, open-label, single-stage, phase 2 nonrandomized controlled trial screened 49 patients and enrolled 36 patients with resectable G/GEJ adenocarcinoma from February 10, 2017, to June 17, 2021, with a median (range) follow-up of 35.2 (17.4-73.0) months. Thirty-four patients were deemed evaluable for efficacy analysis, with 28 (82.4%) undergoing curative resection. This study was performed at 4 referral institutions in the US. Interventions Patients received 3 cycles of capecitabine, 625 mg/m 2 , orally twice daily for 21 days; oxaliplatin, 130 mg/m 2 , intravenously and pembrolizumab, 200 mg, intravenously with optional epirubicin, 50 mg/m 2 , every 3 weeks before and after surgery with an additional cycle of pembrolizumab before surgery. Patients received 14 additional doses of maintenance pembrolizumab. Main Outcomes and Measures The primary end point was pathologic complete response (pCR) rate. Secondary end points included overall response rate, disease-free survival (DFS), overall survival (OS), and safety. Results A total of 34 patients (median [range] age, 65.5 [25-90] years; 23 [67.6%] male) were evaluable for efficacy. Of these patients, 28 (82.4%) underwent curative resection, 7 (20.6%; 95% CI, 10.1%-100%) achieved pCR, and 6 (17.6%) achieved a pathologic near-complete response. Of the 28 patients who underwent resection, 4 (14.3%) experienced disease recurrence. The median DFS and OS were not reached. The 2-year DFS was 67.8% (95% CI, 0.53%-0.87%) and the OS was 80.6% (95% CI, 0.68%-0.96%). Treatment-related grade 3 or higher adverse events for evaluable patients occurred in 20 patients (57.1%), and 12 (34.3%) experienced immune-related grade 3 or higher adverse events. Conclusion and Relevance In this trial of unselected patients with resectable G/GEJ adenocarcinoma, capecitabine, oxaliplatin, and pembrolizumab resulted in a pCR rate of 20.6% and was well tolerated. This trial met its primary end point and supports the development of checkpoint inhibition in combination with perioperative chemotherapy in locally advanced G/GEJ adenocarcinoma. Trial Registration ClinicalTrials.gov Identifier: NCT02918162
Errors in Table 1 and the Results
Journal: JAMA Network Open (2023)

Errors in Table 1 and the ResultsIn the Original Investigation titled "School-Based Health Centers, Access to Care, and Income-Based Disparities," 1 published September 18, 2023, there were transcription errors in Table 1 affecting several percentages and their confidence intervals in the column reporting weighted percentages of counties that did not adopt school-based health centers.There were also 2 transcription errors in the text affecting the confidence intervals of the percentages.This article has been corrected.
Leveraging Tissue-Specific Enhancer–Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer
Authors: Judith Mary Hariprakash, Elisa Salviato, Federica La Mastra, Endre Sebestyén, Ilario Tagliaferri, Raquel Sofia Silva, Federica Lucini, Lorenzo Farina, Mario Cinquanta, Ilaria Rancati, Mirko Riboni, Simone Paolo Minardi, Luca Roz, Francesca Gorini, Chiara Lanzuolo, Stefano Casola, Francesco Ferrari
Journal: Cancer Research (2023)

Abstract Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with the genomic sequence. Enhancer alterations have been associated with various pathological conditions, including cancer. However, the identification and characterization of somatic mutations in noncoding regulatory regions with a functional effect on tumorigenesis and prognosis remain a major challenge. Here, we present a strategy for detecting and characterizing enhancer mutations in a genome-wide analysis of patient cohorts, across three lung cancer subtypes. Lung tissue–specific enhancers were defined by integrating experimental data and public epigenomic profiles, and the genome-wide enhancer–target gene regulatory network of lung cells was constructed by integrating chromatin three-dimensional architecture data. Lung cancers possessed a similar mutation burden at tissue-specific enhancers and exons but with differences in their mutation signatures. Functionally relevant alterations were prioritized on the basis of the pathway-level integration of the effect of a mutation and the frequency of mutations on individual enhancers. The genes enriched for mutated enhancers converged on the regulation of key biological processes and pathways relevant to tumor biology. Recurrent mutations in individual enhancers also affected the expression of target genes, with potential relevance for patient prognosis. Together, these findings show that noncoding regulatory mutations have a potential relevance for cancer pathogenesis and can be exploited for patient classification. Significance: Mapping enhancer–target gene regulatory interactions and analyzing enhancer mutations at the level of their target genes and pathways reveal convergence of recurrent enhancer mutations on biological processes involved in tumorigenesis and prognosis.
Unraveling T-cell Exhaustion: Genetic Screening Meets <i>In Vitro</i> Modeling
Authors: Dominic Schmid, Priska Auf der Maur, Marcel P. Trefny, Alfred Zippelius
Journal: Cancer Research (2023)

Abstract T-cell exhaustion poses a significant barrier to the efficacy of immunotherapies. In the past decade, immune checkpoint blockade (ICB) has been the leading strategy to prevent or reverse T-cell exhaustion. Although ICB yields promising clinical outcomes in patients with cancer, its impact on T-cell reinvigoration is often short-lived. High-throughput genomic tools, including CRISPR screening along with single-cell RNA and chromatin accessibility sequencing may point toward new therapeutic avenues. However, their utility in identifying key mediators of T-cell exhaustion is constrained by the restricted scalability of well-validated in vivo exhaustion models, like chronic LCMV infection. In a recent article in Science Immunology, Wu and colleagues introduce an in vitro exhaustion model that involves repetitive stimulation of T-cell receptor-transgenic, LCMV-specific P14 CD8 T cells. This approach enables a direct comparison of exhausted T (Tex) cells generated both in vivo and in vitro using the same antigen, adeptly pinpointing exhaustion features that can be recapitulated in vitro. Leveraging this efficient and scalable model alongside CRISPR screening, the authors highlight the transcription factor BHLHE40 as a pivotal element in promoting Tex-cell transition from progenitor to intermediate Tex cells.
Multimodal Nanoplatform with ROS Amplification to Overcome Multidrug Resistance in Prostate Cancer via Targeting P‐Glycoprotein and Ferroptosis
Authors: Yupeng Guan, Hanqi Lei, Chengyuan Xing, Binyuan Yan, Bingbiao Lin, Xiangwei Yang, Hai Huang, Yang Kang, Jun Pang
Journal: Advanced Healthcare Materials (2023)

Abstract Chemotherapy remains the most essential treatment for prostate cancer, but multidrug resistance (MDR) contributes to chemotherapy failure and tumor‐related deaths. The overexpression of P‐glycoprotein (P‐gp) is one of the main mechanisms behind MDR. Here, this work reports a multimodal nanoplatform with a reactive oxygen species (ROS) cascade for gas therapy/ferroptosis/chemotherapy in reversing MDR. The nanoplatform disassembles when responding to intracellular ROS and exerts three main functions: First, nitric oxide (NO) targeted delivery can reverse MDR by downregulating P‐gp expression and inhibiting mitochondrial function. Second, ferrocene‐induced ferroptosis breaks the redox balance in the tumor intracellular microenvironment and synergistically acts against the tumor. Third, the release of paclitaxel (PTX) is precisely controlled in situ in the tumor for chemotherapy that avoids damage to normal tissues. Excitingly, this multimodal nanoplatform is a promising weapon for reversing MDR and may provide a pioneering paradigm for synergetic cancer therapy.
<i>MGMT</i> Promoter Methylation and Chemotherapy Outcomes in Low-Grade and Anaplastic Gliomas—Reply
Authors: Connor J. Kinslow, Simon K. Cheng, Tony J. C. Wang
Journal: JAMA Oncology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
Added prognostic value of 3D deep learning-derived features from preoperative MRI for adult-type diffuse gliomas
Authors: Jung Oh Lee, Sung Soo Ahn, Kyu Sung Choi, Junhyeok Lee, Joon Jang, Jung Hyun Park, Inpyeong Hwang, Chul-Kee Park, Sung Hye Park, Jin Wook Chung, Seung Hong Choi
Journal: Neuro-Oncology (2023)

To investigate the prognostic value of spatial features from whole-brain MRI using a three-dimensional (3D) convolutional neural network for adult-type diffuse gliomas.
Suctioning in Bronchiolitis and the Need for More Trials
Authors: Alan R. Schroeder, Shabnam Jain, Shawn L. Ralston
Journal: JAMA Network Open (2023)

Suzanne Schuh, MD; Allan L. Coates, MDCM, BEng; Judy Sweeney, RN, BScN; Maggie Rumantir, MD; Mohamed Eltorki, MBChB, MSc; Waleed Alqurashi, MD, MSc; Amy C. Plint, MD, MSc; Roger Zemek, MD; Naveen Poonai, MD; Patricia C. Parkin, MD; Diane Soares, RRT; Rahim Moineddin, PhD; Yaron Finkelstein, MD; Pediatric Emergency Research Canada (PERC) Network; Redjana Carciumaru ; Kamary CoriolanoDaSilva; Kristina Vogel; Tanveer Colins
<i>MGMT</i> Promoter Methylation and Chemotherapy Outcomes in Low-Grade and Anaplastic Gliomas
Authors: Binghao Zhao, Hao Qi, Wenbin Ma
Journal: JAMA Oncology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
County-Level Trends in Cervical Cancer Incidence, Stage at Diagnosis, and Mortality in Kentucky
Authors: Haluk Damgacioglu, Todd Burus, Kalyani Sonawane, Elizabeth Hill, Krystle A. Lang Kuhs, Ashish A. Deshmukh
Journal: JAMA Network Open (2023)

This cross-sectional study evaluates recent trends in rates of cervical cancer incidence and incidence-based mortality among women in Appalachian and non-Appalachian Kentucky counties.
Reply to Li <i>et al.</i>
Authors: Dinah Foer, Zachary H. Strasser, Jing Cui, Katherine N. Cahill, Joshua A. Boyce, Shawn N. Murphy, Elizabeth W. Karlson
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Reply to: A Daunting and Challenging Task to Prove the Effectiveness of Reducing Acute Exacerbation in COPD Patients with Type 2 Diabetes by GLP-1 Receptor Agonists." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Ecological and environmental factors affecting the risk of tick-borne encephalitis in Europe, 2017 to 2021
Authors: Francesca Dagostin, Valentina Tagliapietra, Giovanni Marini, Claudia Cataldo, Maria Bellenghi, Scilla Pizzarelli, Rosaria Rosanna Cammarano, William Wint, Neil S Alexander, Markus Neteler, Julia Haas, Timothée Dub, Luca Busani, Annapaola Rizzoli
Journal: Eurosurveillance (2023)

Background Tick-borne encephalitis (TBE) is a disease which can lead to severe neurological symptoms, caused by the TBE virus (TBEV). The natural transmission cycle occurs in foci and involves ticks as vectors and several key hosts that act as reservoirs and amplifiers of the infection spread. Recently, the incidence of TBE in Europe has been rising in both endemic and new regions. Aim In this study we want to provide comprehensive understanding of the main ecological and environmental factors that affect TBE spread across Europe. Methods We searched available literature on covariates linked with the circulation of TBEV in Europe. We then assessed the best predictors for TBE incidence in 11 European countries by means of statistical regression, using data on human infections provided by the European Surveillance System (TESSy), averaged between 2017 and 2021. Results We retrieved data from 62 full-text articles and identified 31 different covariates associated with TBE occurrence. Finally, we selected eight variables from the best model, including factors linked to vegetation cover, climate, and the presence of tick hosts. Discussion The existing literature is heterogeneous, both in study design and covariate types. Here, we summarised and statistically validated the covariates affecting the variability of TBEV across Europe. The analysis of the factors enhancing disease emergence is a fundamental step towards the identification of potential hotspots of viral circulation. Hence, our results can support modelling efforts to estimate the risk of TBEV infections and help decision-makers implement surveillance and prevention campaigns.
Tuberculosis incidence in foreign-born people residing in European countries in 2020
Authors: Anca Vasiliu, Niklas Köhler, Ekkehardt Altpeter, Tinna Rán Ægisdóttir, Marina Amerali, Wouter Arrazola de Oñate, Ágnes Bakos, Stefania D’Amato, Daniela Maria Cirillo, Reinout van Crevel, Edita Davidaviciene, Irène Demuth, Jose Domínguez, Raquel Duarte, Gunar Günther, Jean-Paul Guthmann, Sophia Hatzianastasiou, Louise Hedevang Holm, Zaida Herrador, Urška Hribar, Conny Huberty, Elmira Ibraim, Sarah Jackson, Mogens Jensenius, Kamilla Sigridur Josefsdottir, Anders Koch, Maria Korzeniewska-Kosela, Liga Kuksa, Heinke Kunst, Christian Lienhardt, Beatrice Mahler, Mateja Janković Makek, Inge Muylle, Johan Normark, Analita Pace-Asciak, Goranka Petrović, Despo Pieridou, Giulia Russo, Olena Rzhepishevska, Helmut J.F. Salzer, Marta Sá Marques, Daniela Schmid, Ivan Solovic, Mariya Sukholytka, Petra Svetina, Mariya Tyufekchieva, Tuula Vasankari, Piret Viiklepp, Kersti Villand, Jiri Wallenfels, Stefan Wesolowski, Anna-Maria Mandalakas, Leonardo Martinez, Dominik Zenner, Christoph Lange
Journal: Eurosurveillance (2023)

Background European-specific policies for tuberculosis (TB) elimination require identification of key populations that benefit from TB screening. Aim We aimed to identify groups of foreign-born individuals residing in European countries that benefit most from targeted TB prevention screening. Methods The Tuberculosis Network European Trials group collected, by cross-sectional survey, numbers of foreign-born TB patients residing in European Union (EU) countries, Iceland, Norway, Switzerland and the United Kingdom (UK) in 2020 from the 10 highest ranked countries of origin in terms of TB cases in each country of residence. Tuberculosis incidence rates (IRs) in countries of residence were compared with countries of origin. Results Data on 9,116 foreign-born TB patients in 30 countries of residence were collected. Main countries of origin were Eritrea, India, Pakistan, Morocco, Romania and Somalia. Tuberculosis IRs were highest in patients of Eritrean and Somali origin in Greece and Malta (both &gt; 1,000/100,000) and lowest among Ukrainian patients in Poland (3.6/100,000). They were mainly lower in countries of residence than countries of origin. However, IRs among Eritreans and Somalis in Greece and Malta were five times higher than in Eritrea and Somalia. Similarly, IRs among Eritreans in Germany, the Netherlands and the UK were four times higher than in Eritrea. Conclusions Country of origin TB IR is an insufficient indicator when targeting foreign-born populations for active case finding or TB prevention policies in the countries covered here. Elimination strategies should be informed by regularly collected country-specific data to address rapidly changing epidemiology and associated risks.
Errors in Table and Supplement 1
Journal: JAMA Network Open (2023)

Emily G. McDonald, MD, MSc; Gloria Aggrey, MD; Abdullah Tarık Aslan, MD; Michael Casias, PharmD, BCIDP, AAHIVP; Nicolas Cortes-Penfield, MD; Mei Qin (Denise) Dong, PharmD; Susan Egbert, PharmD; Brent Footer, PharmD; Burcu Isler, MD; Madeline King, PharmD; Mira Maximos, PharmD, MSc, ACPR; Terence C. Wuerz, MD, MSc; Ahmed Abdul Azim, MD; Jhongert Alza-Arcila, MD; Anthony D. Bai, MD; Michelle Blyth, MD, MSPH; Tom Boyles, MD; Juan Caceres, MD; Devin Clark, MD; Kusha Davar, MD, MBA, MS; Justin T. Denholm, BMed, PhD; Graeme Forrest, MBBS; Bassam Ghanem, PharmD, MS, BCPS; Stefan Hagel, MD, MS; Alexandra Hanretty, PharmD; Fergus Hamilton, MD; Philipp Jent, MD; Minji Kang, MD; Geena Kludjian, PharmD, BCIDP; Tim Lahey, MD, MMSc; Jonathan Lapin, PharmD; Rachael Lee, MD, MSPH; Timothy Li, MD; Dhara Mehta, PharmD, BCIDP; Jessica Moore, PharmD, MS; Clayton Mowrer, DO, MBA; Georges Ouellet, MD; Rebecca Reece, MD; Jonathan H. Ryder, MD; Alexandre Sanctuaire, PharmD, MSc; James M. Sanders, PharmD, PhD; Bobbi Jo Stoner, PharmD, BCPS; Jessica M. So, MD, MS, MPH; Jean-François Tessier, BSc, MSc; Raghavendra Tirupathi, MD; Steven Y. C. Tong, MBBS, PhD; Noah Wald-Dickler, MD; Arsheena Yassin, PharmD; Christina Yen, MD; Brad Spellberg, MD; Todd C. Lee, MD, MPH